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Peng W, Li Y, Cheng B, Cao M, Liu L, Yang Y, Bai S, Xiong S, Chen W, Zhao Y. Liquid-liquid phase separation-related lncRNA prognostic signature and ZNF32-AS2 as a novel biomarker in hepatocellular carcinoma. Comput Biol Med 2024; 169:107975. [PMID: 38199212 DOI: 10.1016/j.compbiomed.2024.107975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND Liquid-liquid phase separation (LLPS) enhances oncogenic signaling pathways and advances cancer progression, and has been proposed as a promising cancer biomarker and intervention target. Nevertheless, doubts remain about the prognostic importance of LLPS-related long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC). METHODS An LLPS-related lncRNA prognostic signature was generated by drivers and regulators of LLPS, and was validated in external datasets. The underlying genetic changes and functional enrichment of the signature were assessed. The drug sensitivity and response to immunotherapy were predicted in patients categorized as high-risk and low-risk. Clinical samples, phase separation agonist, and dispersant were used to identify lncRNAs with the most significant expression change. Cancer cells with ZNF32-AS2 expression regulation were subjected to colony formation assay, scratch test assay, migration and invasion assay, sorafenib resistance assay, and xenograft tumor model. RESULTS The signature of LLPS-related hub lncRNAs identified through Weighted Gene Co-Expression Network Analysis showed outstanding performance in training and external validation cohorts consistently, and the molecular characteristics varied between different risk groups. Potential drugs for high-risk individuals were identified, and low-risk individuals demonstrated a more favorable reaction to immunotherapy. ZNF32-AS2 showed the most significant expression change in phase separation agonist and dispersant treatment. ZNF32-AS2 promoted the proliferation, mobility, and sorafenib resistance of liver cancer cells. CONCLUSIONS The LLPS-related lncRNA signature may help assess prognosis and predict treatment efficacy in clinical settings. LLPS-related ZNF32-AS2 promoted the proliferation, mobility, and sorafenib resistance of liver cancer cells, and may be a novel potential biomarker in hepatocellular carcinoma.
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Affiliation(s)
- Wang Peng
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanling Li
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bin Cheng
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Mengdie Cao
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Luyao Liu
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yilei Yang
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shuya Bai
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Si Xiong
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Chen
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuchong Zhao
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Chang YS, Tu SJ, Chen HD, Chung CC, Hsu MH, Chou YP, Lee YT, Yen JC, Jeng LB, Chang JG. Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas. Biomark Res 2023; 11:68. [PMID: 37403120 DOI: 10.1186/s40364-023-00492-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/29/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Comprehensive and integrative analysis of hepatocellular carcinoma (HCC) is important. In this study, we explored Taiwanese HCCs using multi-omics analyses. METHODS We analyzed 254 HCCs by whole genome sequencing and total RNA sequencing, and then used bioinformatic tools to analyze genomic and transcriptomic alterations in coding and non-coding sequences to explore the clinical importance of each sequence. RESULTS The frequencies of the five most commonly mutated cancer-related genes were TERT, TP53, CTNNB1, RB1, and ARID1A. Genetic alteration frequencies influenced the etiology of HCC; some alterations were also correlated with clinicopathological conditions. Many cancer-related genes had copy number alterations (CNAs) and structure variants (SVs) that changed according to etiology and exhibited potential associations with survival. We also identified several alterations in histone-related genes, HCC-related long non-coding RNAs, and non-coding driver genes that may contribute to the onset and progression of HCC. Transcriptomic analysis revealed that 229 differentially expressed and 148 novel alternative splicing (AS) genes, as well as the presence of fusion genes, were associated with patient survival. Moreover, somatic mutations, CNAs, and SVs were associated with immune checkpoint gene expression and tumor microenvironment. Finally, we identified relationships among AS, immune checkpoint gene expression and tumor microenvironment. CONCLUSIONS This study shows that genomic alterations are associated with survival, including DNA-based and RNA-based data. Moreover, genomic alterations and their associations with immune checkpoint genes and the tumor microenvironment may provide novel insights for the diagnosis and treatment of HCC.
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Affiliation(s)
- Ya-Sian Chang
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Siang-Jyun Tu
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Hong-Da Chen
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chin-Chun Chung
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
| | - Ming-Hon Hsu
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Pao Chou
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ya-Ting Lee
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
| | - Ju-Chen Yen
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan
| | - Long-Bin Jeng
- Organ Transplantation Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
- School of Medicine, China Medical University, Taichung, Taiwan.
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Candita G, Rossi S, Cwiklinska K, Fanni SC, Cioni D, Lencioni R, Neri E. Imaging Diagnosis of Hepatocellular Carcinoma: A State-of-the-Art Review. Diagnostics (Basel) 2023; 13:diagnostics13040625. [PMID: 36832113 PMCID: PMC9955560 DOI: 10.3390/diagnostics13040625] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains not only a cause of a considerable part of oncologic mortality, but also a diagnostic and therapeutic challenge for healthcare systems worldwide. Early detection of the disease and consequential adequate therapy are imperative to increase patients' quality of life and survival. Imaging plays, therefore, a crucial role in the surveillance of patients at risk, the detection and diagnosis of HCC nodules, as well as in the follow-up post-treatment. The unique imaging characteristics of HCC lesions, deriving mainly from the assessment of their vascularity on contrast-enhanced computed tomography (CT), magnetic resonance (MR) or contrast-enhanced ultrasound (CEUS), allow for a more accurate, noninvasive diagnosis and staging. The role of imaging in the management of HCC has further expanded beyond the plain confirmation of a suspected diagnosis due to the introduction of ultrasound and hepatobiliary MRI contrast agents, which allow for the detection of hepatocarcinogenesis even at an early stage. Moreover, the recent technological advancements in artificial intelligence (AI) in radiology contribute an important tool for the diagnostic prediction, prognosis and evaluation of treatment response in the clinical course of the disease. This review presents current imaging modalities and their central role in the management of patients at risk and with HCC.
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Zhang J, Xun M, Li C, Chen Y. The O-GlcNAcylation and its promotion to hepatocellular carcinoma. Biochim Biophys Acta Rev Cancer 2022; 1877:188806. [PMID: 36152903 DOI: 10.1016/j.bbcan.2022.188806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/27/2022]
Abstract
O-GlcNAcylation is a posttranslational modification that attaches O-linked β-N-acetylglucosamine (O-GlcNAc) to the serine and threonine residues of proteins. Such a glycosylation would alter the activities, stabilities, and interactions of target proteins that are functional in a wide range of biological processes and diseases. Accumulating evidence indicates that O-GlcNAcylation is tightly associated with hepatocellular carcinoma (HCC) in its onset, growth, invasion and metastasis, drug resistance, and stemness. Here we summarize the discoveries of the role of O-GlcNAcylation in HCC and its function mechanism, aiming to deepen our understanding of HCC pathology, generate more biomarkers for its diagnosis and prognosis, and offer novel molecular targets for its treatment.
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Affiliation(s)
- Jie Zhang
- Institute of Pharmacy & Pharmacology, School of Pharmaceutical Science, University of South China, Hengyang 410001, China
| | - Min Xun
- Institute of Pharmacy & Pharmacology, School of Pharmaceutical Science, University of South China, Hengyang 410001, China
| | - Chaojie Li
- Institute of Pharmacy & Pharmacology, School of Pharmaceutical Science, University of South China, Hengyang 410001, China
| | - Yuping Chen
- Institute of Pharmacy & Pharmacology, School of Pharmaceutical Science, University of South China, Hengyang 410001, China.
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Oe N, Takeda H, Eso Y, Takai A, Marusawa H. Clinical and Molecular Basis of Hepatocellular Carcinoma after Hepatitis C Virus Eradication. Pathogens 2022; 11:pathogens11040430. [PMID: 35456105 PMCID: PMC9028726 DOI: 10.3390/pathogens11040430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) arises in the background of chronic liver diseases, including hepatitis and liver cirrhosis caused by hepatitis C virus (HCV) infection. It is well known that HCV eradication using antiviral drugs can efficiently inhibit hepatocarcinogenesis. Recent advances in and development of direct-acting antiviral (DAA) drugs has revolutionized the treatment of HCV infection, and the vast majority of HCV patients can achieve HCV eradication using DAAs. However, mounting evidence clearly indicates that HCC inevitably occurs in a subset of patients after successful viral eradication using DAA therapy. Cancer is a genetic disease, and the accumulation of genetic and epigenetic aberrations may cause hepatocarcinogenesis in chronically damaged liver, even after virus elimination. In this review, we highlight HCC development after HCV eradication and discuss the current understanding of the molecular mechanisms of tumorigenesis after virus elimination, focusing on the genetic and epigenetic background of chronically damaged liver tissues.
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Affiliation(s)
- Natsumi Oe
- Department of Gastroenterology, Red Cross Osaka Hospital, Osaka 5438555, Japan;
| | - Haruhiko Takeda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 6068501, Japan; (H.T.); (Y.E.); (A.T.)
| | - Yuji Eso
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 6068501, Japan; (H.T.); (Y.E.); (A.T.)
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 6068501, Japan; (H.T.); (Y.E.); (A.T.)
| | - Hiroyuki Marusawa
- Department of Gastroenterology, Red Cross Osaka Hospital, Osaka 5438555, Japan;
- Correspondence: ; Tel.: +81-6-6774-5111; Fax: +81-6-6774-5131
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